Re: [Nemo2-user] shared genetic map

[Fred G. <gui...@gm...>]

Dear Nathan,

Thanks!

To solve your problem, you could add one (or two) "neutral" QTL on the
last chromosome.

To do so, you'd have to have di-allelic loci and set the allelic effects
to 0 for the QTL on chromosome 6, with something like:

quanti_loci         11
quanti_allele_model diallelic_HC
quanti_allele_value {{a, a, a, a, a, a, a, a, a, a, 0}}
#   alleles have value +/- a (loc 1 - 10) or 0 (loc 11)
quanti_chromosome_num_locus {{2, 2, 2, 2, 2, 1}}
...

that should work! tell us if not (I haven't tested it)

On the other hand, there is no way around this limitation if you can't
simulate di-allelic loci, because there is no locus-specific mutation
model for the continuous allele model (yet).

I hope this helps.

Best,
Fred


On 8/24/20 3:10 PM, Nathan White wrote:
> Dear Fred (et al)
> 
> I'm a PhD student at the University of Sheffield and have been using
> Nemo for a few months now- it's very useful, thank you very much for
> developing it!
> 
> I've encountered a problem with the genetic map- I'm trying to simulate
> 6 chromosomes with 100 neutral sites each, then place 2 quant loci on
> each chromosome except for one (so it has only neutral sites). 
> 
> My code has the relevant lines, e.g.
> ntrl_loci 600
> ntrl_random_genetic_map {{100, 100, 100, 100, 100, 100}}
> 
> quanti_random_genetic_map {{100, 100, 100, 100, 100, 100}} 
> quanti_chromosome_num_locus {{2, 2, 2, 2, 2, 0}}
> quanti_loci 10
> 
> But when I run it, I get the error 
> ***ERROR*** the genetic map doesn't accept empty chromosomes with 0 loci
> ***ERROR*** initialization of prototype for trait "quant" failed
> 
> Is there a way around this? To have a chromosome with neutral loci but
> no quanti loci?
> 
> Thanks very much
> Nathan
> -- 
> Nathan White
> PhD Student
> Dept. Animal & Plant Sciences
> University of Sheffield
> @NJWhite_Evo
> 
> 
> 
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